Is KIT c.*790A>G pathogenic?

KIT c.790A>G is classified Benign/Likely benign in KIT (ClinVar, Single submitter, 1 submitter; last evaluated 2018-01-13). Rare (popmax 0.196%, amr); Associated with mastocytosis.

What condition is associated with KIT c.*790A>G?

KIT c.*790A>G is associated with mastocytosis, piebaldism, gastrointestinal stromal tumor (ClinVar).

How common is KIT c.*790A>G in the general population?

KIT c.*790A>G is rare (popmax 0.196%, amr) (gnomAD).

KIT c.*790A>G

rs189995563 · VCV348965

Benign/Likely benign Single submitter

Classification

Benign/Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.196%, amr)

Conditions

mastocytosis

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2	GERP -2.3, phastCons 0.64
Non-coding constraint	Z -0.23	1 kb window · o/e 1.02 · regional · uncalibrated
Overall
CADD	7.157	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.196% Admixed American · 35/17,830 alleles

Filtering AF 0.145% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.127%

Overall 0.0635% 149/234,820 alleles · rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.196%	509
Remaining individualsnot grpmax-eligible	0.112%	892
European (non-Finnish)	0.0791%	1,265
African / African-American	0.0198%	5,059
Finnishnot grpmax-eligible	0.00893%	11,198

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: KIT
Coding: c.*790A>G
MANE Select: NM_000222
dbSNP: rs189995563
Type: single nucleotide variant
Location: chr4:54739347 (GRCh38)
Gene constraint: LOEUF 0.24 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 78.52 · 65 PDB

Full KIT gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

mastocytosis — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: piebaldism gastrointestinal stromal tumor

Similar variants

KIT p.Ala621Thr Pathogenic/Likely pathogenic ★★ same condition
KIT p.Asp820Tyr Pathogenic ★★ same condition
KIT p.Gln190Ter Pathogenic ★★ same condition
KIT p.Leu576Pro Pathogenic/Likely pathogenic ★★ same condition
KIT p.Lys642Glu Pathogenic ★★ same condition
KIT p.Trp557Arg Pathogenic/Likely pathogenic ★★ same condition
KIT p.Val559Ala Pathogenic/Likely pathogenic ★★ same condition
KIT c.1232-3T>C Uncertain significance ★★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/kit-c-star-790a-g (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown